After running this minimization when i did gmxcheck i got this output trn version: GMX_trn_file (single precision) Reading frame 0 time 9.000 # Atoms 4113 Reading frame 3 time 57.000 Timesteps at t=31 don't match (12, 26) Reading frame 4 time 69.000 Timesteps at t=57 don't match (26, 12) Reading frame 14 time 192.000 Timesteps at t=184 don't match (13, 8) Last frame 14 time 192.000
Item #frames Step 15 Time 15 Lambda 15 Coords 15 Velocities 0 Forces 0 Box 15 why is it saying that Timesteps at t=31 don't match (12, 26). On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 21/10/2011 5:09 PM, aiswarya pawar wrote: > >> Hi users, >> >> Iam running a minimization on protein complex in vacuum. i have set the >> parameters as following- >> >> ; Lines starting with ';' ARE COMMENTS >> ; Everything following ';' is also comment >> >> title = Energy Minimization ; Title of run >> >> ; The following line tell the program the standard locations where to find >> certain files >> cpp = /lib/cpp ; Preprocessor >> >> >> ; Define can be used to control processes >> define = -DFLEXIBLE >> >> ; Parameters describing what to do, when to stop and what to save >> integrator = steepest ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force < >> 1.0 kJ/mol >> emstep = 0.01 >> nsteps = 50000 ; Maximum number of (minimization) steps to >> perform >> nstenergy = 1 ; Write energies to disk every nstenergy steps >> energygrps = Protein ; Which energy group(s) to write to disk >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstxout = 1 >> nstlist = 10 ; Frequency to update the neighbor list and >> long range forces >> ns_type = grid ; Method to determine neighbor list (simple, >> grid) >> rlist = 1.0 ; Cut-off for making neighbor list (short range >> forces) >> coulombtype = cutoff ; Treatment of long range electrostatic >> interactions >> rcoulomb = 1.0 ; long range electrostatic cut-off >> rvdw = 1.4 ; long range Van der Waals cut-off >> constraints = none ; Bond types to replace by constraints >> pbc = no ; Periodic Boundary Conditions (yes/no) >> >> But from this i could write only 2 frames i need to increase the time >> frames, what is to be changed in the parameters. >> > > This will write every frame of the EM, but if it only has two steps... > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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